The US military covered up a reported surface-to-air missile strike by the Taliban that shot down a Chinook helicopter over Helmand in 2007 and killed seven soldiers, including a British military photographer, the war logs show.

The strike on the twin-rotor helicopter shows the Taliban enjoyed sophisticated anti-aircraft capabilities earlier than previously thought, casting new light on the battle for the skies over Afghanistan.

Hundreds of files detail the efforts of insurgents, who have no aircraft, to shoot down western warplanes. The war logs detail at least 10 near-misses by missiles in four years against coalition aircraft, one while refuelling at 11,000ft and another involving a suspected Stinger missile of the kind supplied by the CIA to Afghan rebels in the 1980s.

But if American and British commanders were worried about the missile threat, they downplayed it in public – to the extent of ignoring their own pilots' testimony. The CH-47 Chinook was shot down on 30 May 2007 after dropping troops at the strategic Kajaki dam in Helmand where the British were leading an anti-Taliban drive. Witnesses reported that a missile struck the left rear engine of the aircraft, causing it to burst into flames and nosedive into the ground. All on board died, including 28-year-old Corporal Mike Gilyeat of the Royal Military Police.

Later that day Nato and US officials suggested the helicopter, codenamed Flipper, had been brought down by a rocket-propelled grenade – effectively, a lucky hit. "It's not impossible for small-arms fire to bring down a helicopter," Nato spokesman Major John Thomas told Reuters in Kabul. A US official said it had "probably been brought down by a rocket-propelled grenade [RPG]".

But US pilot logs show they were certain the missile was not an RPG and was most likely a Manpad – the military term for a shoulder-launched surface-to-air missile. "Witness statements from Chalk 3 [another aircraft] suggest Flipper was struck by Manpad," it reads.

Those fears were confirmed by two Apache attack helicopters hovering over the crash site that came under fire from more missiles, twice in 30 minutes. Both missiles missed, and the pilots subsequently reported that they were "not an RPG" but a "probable first-generation MANPAD".

The crash and its handling highlight steadily escalating US worries amid a stream of intelligence reports, also captured in the files, that suggest the Taliban were being supplied with missiles from Iran and Pakistan.

One internal report in September 2005 warned that Taliban commanders in Zabul and Kandahar provinces had acquired missiles they called "number two Stinger", for about $1,000 (£650) each. Nine months later came the first of at least 10 near-miss reports.

In June 2006 a Black Hawk medevac helicopter came under fire 25 miles from Kandahar. The missile changed course after the American crew launched six diversionary flares. "The crew chief saw only the smoke trail due to evasive maneuvering but determined that the missile was a type of MANPAD," the subsequent report read – the second Manpad attack that month.

In June 2007, shortly after the American Chinook was shot down in Kajaki, a British Chinook had a close shave when its missile warning system activated 6,000ft over Helmand. "The crew looked out their window and observed a projectile with a white-grey tight spiral smoke trail rising from their 7 o'clock, climbing through their level and exploding 2000ft 3000ft above and 0.5-1nm [nautical miles] ahead of the aircraft," it read.

A month later a C-130 aircraft was refueling 11,000ft over Nimroz province when a crew member spotted a "bright flash" followed by a second flash 2 nautical miles away. "A corkscrew smoke trale [sic] was observed and the aircraft dispensed flares" just before projectiles streaked past the plane, read the assessment.

The anti-aircraft missile threat has a strong historical resonance in Afghanistan. CIA-supplied Stingers punched dozens of Soviet Hind helicopters from the skies in the 1980s, and were considered to have played a key role in forcing the Soviets to abandon the country in 1989.

Western worries that the phenomenon could be repeated in this war have made surface-to-air missiles a favourite topic among intelligence informers, whose unconfirmed accounts of meddling foreign powers stuff the files.

More concretely, the files contain first-hand accounts of Afghan tribesmen slipping into US bases offering to sell their private stock of missiles. In one instance four elders from Balkh, near Mazar-i-Sharif, arrived with a clutch of blurry photographs of missiles. "Their motivation is monetary gain," the report notes.

The Americans were particularly interested in retrieving unused Stingers from the stockpile of up to 2,000 distributed in the 1980s. One report from Jowzjan in 2005 said an Afghan intelligence chief was authorised to pay $5,000 for older SA-7 missiles and $15,000 for a Stinger. "The NDS [National Directorate of Security] had been ordered to buy all they can acquire, to stop them falling into OMF [opposing military force] hands," it says.

Military experts say many Stingers may no longer be operational – due to drained batteries, for instance – but on at least one occasion US troops feared they were under fire from their own weapons. A Black Hawk helicopter leaving an airbase in Paktika province in July 2007 came under fire from two missiles that crew members believed were Stingers. It was a "probable Stinger due to flight characteristics, the smoke trail going straight up, then turn towards aircraft and lack of cork screws".

The assessment was provided by a crew member who said he had previously operated the Stinger system. It is not recorded whether his assessment was later confirmed.

Another eye-catching intelligence report from January 2009 says an Iranian agent, Hussein Razza, had arrived in Marjah in Helmand carrying four Stingers. There have been no reports since of aircraft being shot down in Marjah, where British and American troops launched a major offensive last February.

But for all the worries about Manpads and Stingers, the Taliban's most potent weapon against US aircraft was a carefully aimed RPG. In June 2005 a Taliban rocket shot down a Chinook in Kunar, killing all 16 special forces troops on board. Another RPG strike in 2007 forced a Black Hawk in Wardak province to crash-land.

As fighting surged in the runup to the last election in August 2009, one report noted 32 RPG attacks against aircraft across Afghanistan in the previous month. "RPGs remain the most lethal weapon system used in theatre, accounting for the majority of A/C [aircraft] losses," it said.

But some missile attacks remained a mystery. In August 2007 two Harrier jets flying at 270mph were circling a target when "an unidentified rocket" passed between them, leaving a thick smoke trail that soared above 21,000ft and took three minutes to dissipate. Task Force Pegasus, the US army aviation command, was puzzled. "The signature reported by the crew does not match any known weapon in Afghanistan. Every MANPAD and known rockets burn out at half the height reported by the crew."